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- PDB-3oa9: Effector domain of influenza A/Duck/Albany/76 NS1 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 3oa9
TitleEffector domain of influenza A/Duck/Albany/76 NS1
ComponentsNon-structural protein 1
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


symbiont-mediated suppression of host mRNA processing / symbiont-mediated suppression of host PKR/eIFalpha signaling / protein serine/threonine kinase inhibitor activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / RNA binding
Similarity search - Function
Influenza virus non-structural protein, effector domain / Influenza A virus NS1 protein / Influenza A virus NS1, effector domain-like superfamily / Influenza non-structural protein (NS1) / Influenza non-structural protein (NS1) / Nucleotidyltransferase; domain 5 / S15/NS1, RNA-binding / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Non-structural protein 1
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKerry, P.S. / Lewis, A. / Hale, B.G. / Hass, C. / Taylor, M.A. / Randall, R.E. / Russell, R.J.M.
CitationJournal: Plos One / Year: 2011
Title: A Transient Homotypic Interaction Model for the Influenza A Virus NS1 Protein Effector Domain.
Authors: Kerry, P.S. / Ayllon, J. / Taylor, M.A. / Hass, C. / Lewis, A. / Garcia-Sastre, A. / Randall, R.E. / Hale, B.G. / Russell, R.J.
History
DepositionAug 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Non-structural protein 1
B: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)35,5092
Polymers35,5092
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.956, 47.956, 231.535
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Non-structural protein 1 / NS1 / NS1A


Mass: 17754.348 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Duck/Alberta/60/1976 H12N5 / Gene: NS / Production host: Escherichia coli (E. coli) / References: UniProt: P69270
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.17 %

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.9→28.27 Å / Num. obs: 6633

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.6_289) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→28.27 Å / SU ML: 0.59 / σ(F): 1.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3381 315 4.75 %
Rwork0.22 --
obs0.2252 6633 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.763 Å2 / ksol: 0.296 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.7436 Å2-0 Å2-0 Å2
2--5.7436 Å20 Å2
3----11.4872 Å2
Refinement stepCycle: LAST / Resolution: 2.9→28.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 0 16 1808
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011820
X-RAY DIFFRACTIONf_angle_d1.3442456
X-RAY DIFFRACTIONf_dihedral_angle_d17.939684
X-RAY DIFFRACTIONf_chiral_restr0.077282
X-RAY DIFFRACTIONf_plane_restr0.005314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.65040.39911530.26533146X-RAY DIFFRACTION99
3.6504-28.27090.30481620.19553172X-RAY DIFFRACTION100

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